Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2892
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57529
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:256 original size:18 final size:18
Alignment explanation
Indices: 235--273 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
225 CTTTTTTGGA
235 GGAGGT-TTTGTTTTTTTT
1 GGAGGTGTTT-TTTTTTTT
253 GGAGGTGTTTTTTTTTTT
1 GGAGGTGTTTTTTTTTTT
271 GGA
1 GGA
274 AAAAATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (18 bp):
GGAGGTGTTTTTTTTTTT
Found at i:257 original size:21 final size:21
Alignment explanation
Indices: 206--270 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
196 AGGTTTTTGG
* *
206 TTTTTGGAGAAGG-ATTGTTCT
1 TTTTTGGAGGAGGTTTTGTT-T
227 TTTTTGGAGGAGGTTTTGTTT
1 TTTTTGGAGGAGGTTTTGTTT
*
248 TTTTTGGAGG-TGTTTT-TTT
1 TTTTTGGAGGAGGTTTTGTTT
267 TTTT
1 TTTT
271 GGAAAAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
21 23 0.57
22 5 0.12
ACGTcount: A:0.11, C:0.02, G:0.28, T:0.60
Consensus pattern (21 bp):
TTTTTGGAGGAGGTTTTGTTT
Found at i:632 original size:24 final size:23
Alignment explanation
Indices: 600--680 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
590 CTTTGTTTTA
*
600 TTATTTTATTATTTTTACTATTAT
1 TTATATTATTATTTTTA-TATTAT
* *
624 TTATATTATTATTATTATTTCTCAT
1 TTATATTATTATTTTTATAT-T-AT
649 TGTATATTA-T-TTTTTATATTAT
1 T-TATATTATTATTTTTATATTAT
671 ATTATATTAT
1 -TTATATTAT
681 ATATGCCCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 9 0.19
23 4 0.09
24 23 0.49
25 4 0.09
26 7 0.15
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATATTATTATTTTTATATTAT
Found at i:659 original size:3 final size:3
Alignment explanation
Indices: 597--642 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
587 GAGCTTTGTT
* *
597 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
641 TT
1 TT
643 TCTCATTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 3 0.08
3 32 0.89
4 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:935 original size:17 final size:18
Alignment explanation
Indices: 882--937 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
872 ACTATTACTA
*
882 TTATATATTAGTGTATATT
1 TTATATA-TAGTATATATT
*
901 TT-TATGTA-TATATATT
1 TTATATATAGTATATATT
917 TTATATATAGTAT-TATT
1 TTATATATAGTATATATT
934 TTAT
1 TTAT
938 TACTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 9 0.28
17 15 0.47
18 6 0.19
19 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (18 bp):
TTATATATAGTATATATT
Found at i:1031 original size:12 final size:12
Alignment explanation
Indices: 1014--1043 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1004 GTGTATTTCT
1014 TATATACATATA
1 TATATACATATA
*
1026 TATATACATTTA
1 TATATACATATA
1038 TATATA
1 TATATA
1044 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:12126 original size:44 final size:44
Alignment explanation
Indices: 11949--12496 Score: 401
Period size: 44 Copynumber: 12.5 Consensus size: 44
11939 TCATTAAAGT
* * *
11949 AGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
* * * ** * * *
11993 AGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAGGAT-GC
1 AGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAGATAGC
* * * * *
12036 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* * *
12081 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGC
1 AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
* * * * *
12125 AGATCCTATCTTTCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* * * * * *
12168 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGT
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* *
12213 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
* * * ** * * *
12257 AGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAATAT-GC
1 AGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAGATAGC
* * * * * *
12300 AGATCTTGTCTTCCCATATTGGTGGCGAAATAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* *
12345 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
* * * ** * *
12389 AGGTCCTATCTTCCTATATTGATAG-GAAGTCGATCCAAGAT-GC
1 AGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAGATAGC
* * * * * *
12432 AGATCTTGTCTTCCCATACTGGTGGTAAAGTAGATTGAAGATTGC
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* *
12477 AGATCTTGCCTTCCTGTATT
1 AGATCTTGTCTTCCTATATT
12497 TGGCAGCGAA
Statistics
Matches: 380, Mismatches: 109, Indels: 29
0.73 0.21 0.06
Matches are distributed among these distances:
43 81 0.21
44 215 0.57
45 84 0.22
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (44 bp):
AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
Found at i:12186 original size:132 final size:132
Alignment explanation
Indices: 11944--12496 Score: 917
Period size: 132 Copynumber: 4.2 Consensus size: 132
11934 TAAAGTCATT
* *
11944 AAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
12009 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
12074 AG
131 AG
* * *
12076 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
12141 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
12206 AG
131 AG
*
12208 AAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
12273 TATTGATAGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAATAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
12338 AG
131 AG
12340 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * ** * *
12405 TATTGATAGGAAGTCGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGTAAAGTAGATTGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
12470 AG
131 AG
** * *
12472 ATTGCAGATCTTGCCTTCCTGTATT
1 AAAGCAGATCTTGTCTTCATGTATT
12497 TGGCAGCGAA
Statistics
Matches: 392, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 392 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
AG
Found at i:12644 original size:134 final size:134
Alignment explanation
Indices: 12462--13436 Score: 1689
Period size: 134 Copynumber: 7.3 Consensus size: 134
12452 GGTGGTAAAG
* **
12462 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATTAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
* * *
12527 TTTACCTCCCTGACCACAGTGGAGTACACTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGT
66 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
12592 GGAA
131 GGAA
* * *
12596 TAGATTGAATATTGCAGATCTTACCTTCCTGTATTCGGCAGTGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
* *
12661 TTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAGT
66 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
12726 GGAA
131 GGAA
*
12730 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
* * *
12795 TTTACCTCCCTGACCACAGTGGAGTACACTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGT
66 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
12860 GGAA
131 GGAA
* * *
12864 TAGATTGAAGATTGCAGATCTTGCCTTCCTATATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
12929 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
66 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
12994 GGAA
131 GGAA
* *
12998 TAGATTGAATATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATTGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
13063 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
66 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
13128 GGAA
131 GGAA
*
13132 TAGATTGAATATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
* *
13197 TTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAGT
66 TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
13262 GGAA
131 GGAA
*
13266 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
*
13331 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
66 TTTACCTCCC--TGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
13396 GTGGAA
129 GTGGAA
* *
13402 TAGATTGAAGATTGCAGATCCTGCCTTCCTATATT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATT
13437 GGTAGGAAGT
Statistics
Matches: 800, Mismatches: 39, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
134 709 0.89
136 91 0.11
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (134 bp):
TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGAT
TTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGT
GGAA
Found at i:13650 original size:40 final size:40
Alignment explanation
Indices: 13598--13749 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
13588 AAGATTACAA
* *
13598 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*** *
13638 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCATAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCA-AG
* * *
13679 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
13720 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
13750 CTAAAAACAC
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:13683 original size:82 final size:83
Alignment explanation
Indices: 13597--13755 Score: 257
Period size: 82 Copynumber: 1.9 Consensus size: 83
13587 GAAGATTACA
* * * *
13597 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTAGTGG
1 ATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGG
13662 AGCAGA-TAAAACCATAG
66 AGCAGACTAAAACCATAG
* *
13679 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTGG
1 ATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGG
13744 AGCAGACTAAAA
66 AGCAGACTAAAA
13756 ACACAAATCT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 65 0.93
83 5 0.07
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (83 bp):
ATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGG
AGCAGACTAAAACCATAG
Found at i:14268 original size:23 final size:23
Alignment explanation
Indices: 14210--14291 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
14200 AGAGGGTGGG
* *
14210 TTTTTGGTTTTTTGGAGAAGGATT
1 TTTTTTGTTTTTTGGAGGAGG-TT
*
14234 GTTCTTTG--TTTTGGAGGAGGTT
1 -TTTTTTGTTTTTTGGAGGAGGTT
**
14256 TTTTTTGTTTTTT-TTGGAGGTGT
1 TTTTTTGTTTTTTGGAGGAGGT-T
14279 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
14292 TGGAAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.12
22 8 0.17
23 29 0.60
25 5 0.10
ACGTcount: A:0.09, C:0.01, G:0.27, T:0.63
Consensus pattern (23 bp):
TTTTTTGTTTTTTGGAGGAGGTT
Found at i:14272 original size:25 final size:23
Alignment explanation
Indices: 14242--14292 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 23
14232 TTGTTCTTTG
14242 TTTTGGAGGAGGTTTTTTTTGTTTT
1 TTTTGGAGG-GG-TTTTTTTGTTTT
*
14267 TTTTGGAGGTGTTTTTTTGTTTT
1 TTTTGGAGGGGTTTTTTTGTTTT
14290 TTT
1 TTT
14293 GGAAAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.60
24 1 0.04
25 9 0.36
ACGTcount: A:0.06, C:0.00, G:0.25, T:0.69
Consensus pattern (23 bp):
TTTTGGAGGGGTTTTTTTGTTTT
Found at i:14274 original size:22 final size:23
Alignment explanation
Indices: 14249--14292 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
14239 TTGTTTTGGA
14249 GGAGGT-TTTTTTTGTTTTTTTT
1 GGAGGTGTTTTTTTGTTTTTTTT
14271 GGAGGTGTTTTTTTGTTTTTTT
1 GGAGGTGTTTTTTTGTTTTTTT
14293 GGAAAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.05, C:0.00, G:0.25, T:0.70
Consensus pattern (23 bp):
GGAGGTGTTTTTTTGTTTTTTTT
Found at i:14637 original size:3 final size:3
Alignment explanation
Indices: 14623--14708 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
14613 GAGCTTTGTT
* *
14623 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
14667 TT- TCTCA TGTA TATA TTA TT- TT- TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
14709 ATATGCCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 12 0.18
3 48 0.71
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:14665 original size:18 final size:18
Alignment explanation
Indices: 14623--14712 Score: 83
Period size: 18 Copynumber: 4.7 Consensus size: 18
14613 GAGCTTTGTT
*
14623 TTATTATTTTATTATTTTTA
1 TTATTA-TTTA-TATTATTA
*
14643 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
14661 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
*
14682 TTATTTTTTATATTATTA
1 TTATTATTTATATTATTA
14700 TTA-TATTATATAT
1 TTATTATT-TATAT
14713 GCCCTCTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 3 0.05
18 26 0.44
19 9 0.15
20 10 0.17
21 11 0.19
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:14950 original size:18 final size:19
Alignment explanation
Indices: 14914--14972 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
14904 ACTATTACTA
*
14914 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
14934 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
14951 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
14969 TTAT
1 TTAT
14973 TACTTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 2 0.06
20 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:14954 original size:17 final size:18
Alignment explanation
Indices: 14914--14969 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
14904 ACTATTACTA
*
14914 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATA-TT
*
14934 TTATGTATA-TATATATT
1 TTATATATAGTATATATT
14951 TTATATATAGTAT-TATT
1 TTATATATAGTATATATT
14968 TT
1 TT
14970 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 16 0.50
18 8 0.25
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (18 bp):
TTATATATAGTATATATT
Found at i:17816 original size:13 final size:13
Alignment explanation
Indices: 17807--17833 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17797 TATTAATATG
17807 ATAATATAATAAA
1 ATAATATAATAAA
17820 ATAATATAATAAA
1 ATAATATAATAAA
17833 A
1 A
17834 CATAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATATAATAAA
Found at i:17831 original size:8 final size:8
Alignment explanation
Indices: 17783--17825 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
17773 GTACTTAAGT
17783 ATAATATA
1 ATAATATA
*
17791 AGAATATA
1 ATAATATA
* *
17799 TTAATATG
1 ATAATATA
17807 ATAATATA
1 ATAATATA
*
17815 ATAAAATA
1 ATAATATA
17823 ATA
1 ATA
17826 TAATAAAACA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (8 bp):
ATAATATA
Found at i:19137 original size:16 final size:15
Alignment explanation
Indices: 19091--19139 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
19081 GGATGATGAG
19091 TTTTATGAAATTGATTA
1 TTTTATG-AA-TGATTA
*
19108 TTTTTTGAATGATTA
1 TTTTATGAATGATTA
*
19123 TTATTATGTATGATTA
1 TT-TTATGAATGATTA
19139 T
1 T
19140 GTATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.29
16 14 0.50
17 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTTATGAATGATTA
Found at i:23903 original size:22 final size:22
Alignment explanation
Indices: 23878--23927 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
23868 AACATTCCTG
*
23878 AATGGAAAT-GAGACTGCATTAC
1 AATGGAAATAG-GAATGCATTAC
23900 AATGGAAATAGGAATGCATTAC
1 AATGGAAATAGGAATGCATTAC
23922 AATGGA
1 AATGGA
23928 CATGGGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (22 bp):
AATGGAAATAGGAATGCATTAC
Found at i:25107 original size:13 final size:13
Alignment explanation
Indices: 25077--25101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25067 AGAACATGGG
25077 AGAAAGAAAAAAA
1 AGAAAGAAAAAAA
25090 AGAAAGAAAAAA
1 AGAAAGAAAAAA
25102 TGGAAATTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAAAA
Found at i:33291 original size:20 final size:21
Alignment explanation
Indices: 33260--33299 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
33250 TTTTACTTTC
*
33260 CATAATCTCAATATCGCATTT
1 CATAATCTCAATATCACATTT
33281 CATAA-CTCAATATCACATT
1 CATAATCTCAATATCACATT
33300 CACTTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (21 bp):
CATAATCTCAATATCACATTT
Found at i:33341 original size:37 final size:37
Alignment explanation
Indices: 33284--33358 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
33274 CGCATTTCAT
* * *
33284 AACTCAATATCACATTCACTTTAGTTATCTATTAATC
1 AACTCAATATCACATCCACTTCAATTATCTATTAATC
*
33321 AACTCAATATCATATCCACTTCAATTATCTATTAATC
1 AACTCAATATCACATCCACTTCAATTATCTATTAATC
33358 A
1 A
33359 TTCATTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (37 bp):
AACTCAATATCACATCCACTTCAATTATCTATTAATC
Found at i:36439 original size:40 final size:40
Alignment explanation
Indices: 36384--36594 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
36374 ATTTGAATGA
*
36384 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
36424 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
36464 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
36504 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
36544 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
36584 TATCC-GGCTAA
1 TATCCGGGCTAA
36595 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:44598 original size:40 final size:40
Alignment explanation
Indices: 44544--44753 Score: 230
Period size: 40 Copynumber: 5.3 Consensus size: 40
44534 ATTTGAATGA
*
44544 TATCC-GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
44583 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
44623 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
44663 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
44703 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
44743 TATCC-GGCTAA
1 TATCCGGGCTAA
44754 ATTCCGAAGA
Statistics
Matches: 155, Mismatches: 12, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
39 12 0.08
40 140 0.90
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:47067 original size:314 final size:314
Alignment explanation
Indices: 46489--47079 Score: 1074
Period size: 314 Copynumber: 1.9 Consensus size: 314
46479 CTTAGCTGCT
* *
46489 CTGTAATAGTCCGATTTAGAACCTAGTCAGAATAGTGGTTTTGGGACCCCATATCCGAGTCAAAA
1 CTGTAACAATCCGATTTAGAACCTAGTCAGAATAGTGGTTTTGGGACCCCATATCCGAGTCAAAA
* * **
46554 TAATATTTAAATATTATTCTCCGTGTTCATGATGTGTGAATTAGTATGTGTGAAAGTTTTTTTTG
66 TAATATTTAAATATTATTCCCCGTGTTCATGATGTGTGAATTAGTATGCGTGAAAGTTTCGTTTG
46619 AAAATTTAACTATTTGTGTGCTTAATTTGCAAAAAGGACCTAATCACGTAAAGTGTAAAAGCTGT
131 AAAATTTAACTATTTGTGTGCTTAATTTGCAAAAAGGACCTAATCACGTAAAGTGTAAAAGCTGT
*
46684 GTGCTAGATGTTAAAGCTCCTATTTGAGTTGGATTTCTAAAGCAAGGGTCCTTATGTTGTTATTT
196 GTGCTAGATGTTAAAGCACCTATTTGAGTTGGATTTCTAAAGCAAGGGTCCTTATGTTGTTATTT
46749 GTCCATTGAAAATGTTAGAAGATGTTATGATACAACAATATCCAAAGCGGAGAA
261 GTCCATTGAAAATGTTAGAAGATGTTATGATACAACAATATCCAAAGCGGAGAA
* * *
46803 CTGTAACAATCCGATTTAGACCCTAGTCGGAATAGTGGTTTTGGGACCCCATATCCGATTCAAAA
1 CTGTAACAATCCGATTTAGAACCTAGTCAGAATAGTGGTTTTGGGACCCCATATCCGAGTCAAAA
46868 TAATATTTAAATATTATTCCCCGTGTTCATGATGTGTGAATTAGTATGCGTGAAAGTTTCGTTTG
66 TAATATTTAAATATTATTCCCCGTGTTCATGATGTGTGAATTAGTATGCGTGAAAGTTTCGTTTG
*
46933 AAAATTTAACTATTTGTGTGCTTAATTTGCAAAAAGGACCTAATCGCGTAAAGTGTAAAAGCTGT
131 AAAATTTAACTATTTGTGTGCTTAATTTGCAAAAAGGACCTAATCACGTAAAGTGTAAAAGCTGT
*
46998 GTGCTAGATGTTAAAGCACCTATTTGAGTTGGCTTTCTAAAGCAAGGGTCCTTATGTTGTTATTT
196 GTGCTAGATGTTAAAGCACCTATTTGAGTTGGATTTCTAAAGCAAGGGTCCTTATGTTGTTATTT
47063 GTCCATTGAAAATGTTA
261 GTCCATTGAAAATGTTA
47080 ATGGACTAAA
Statistics
Matches: 265, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
314 265 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (314 bp):
CTGTAACAATCCGATTTAGAACCTAGTCAGAATAGTGGTTTTGGGACCCCATATCCGAGTCAAAA
TAATATTTAAATATTATTCCCCGTGTTCATGATGTGTGAATTAGTATGCGTGAAAGTTTCGTTTG
AAAATTTAACTATTTGTGTGCTTAATTTGCAAAAAGGACCTAATCACGTAAAGTGTAAAAGCTGT
GTGCTAGATGTTAAAGCACCTATTTGAGTTGGATTTCTAAAGCAAGGGTCCTTATGTTGTTATTT
GTCCATTGAAAATGTTAGAAGATGTTATGATACAACAATATCCAAAGCGGAGAA
Found at i:54851 original size:40 final size:40
Alignment explanation
Indices: 54814--54998 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
54804 GCTACTCGTT
*
54814 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
54854 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
54894 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
54934 CAAATGCCTT--GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
54974 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54999 CATCATTCAA
Statistics
Matches: 129, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
39 27 0.21
40 97 0.75
41 5 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Done.